[gmx-users] Calculating diffusion coefficient in three dimension

[Venkat Reddy]

Dear Sir, Thanks for the quick reply.
So, I have to declare -type no flag. Isn't it??
and I have recently gone through Justin's membrane protein tutorial, where
he has calculated diffusion coefficient for lipids in a membrane by
creating an index group for a particular atom. So, here also shall I do the
same thing? Moreover, mine is a coarse-grained system.



On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/12/13 11:25 AM, Venkat Reddy wrote:
>
>> Then, how to mention the direction for spherical particles Sir?
>>
>>
> Read g_msd -h again, paying specific attention to the -type flag.
>
>
> -Justin
>
>
>> On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 11/12/13 8:55 AM, Venkat Reddy wrote:
>>>
>>>  Thank you sir for the prompt reply.
>>>> *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns*
>>>>
>>>> Here I am giving -lateral z (like for membrane simulations). Is it fine
>>>> for
>>>> spherical systems also?
>>>>
>>>>
>>>>
>>>>  No.  The system is a sphere, so what use is it to calculate motion
>>> perpendicular to z when you have lipids moving in all three spatial
>>> dimensions?  A vesicle is very different from a membrane, in which the
>>> lipids move in a plane, thus making "-lateral z" useful.
>>>
>>> -Justin
>>>
>>>
>>>   On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban <vvchaban at gmail.com
>>>
>>>> wrote:
>>>>>
>>>>
>>>>   MSD is 3D by default.
>>>>
>>>>>
>>>>>
>>>>> Dr. Vitaly V. Chaban
>>>>>
>>>>>
>>>>> On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy <venkat4bt at gmail.com>
>>>>> wrote:
>>>>>
>>>>>  Dear all,
>>>>>> I am simulating a spherical lipid vesicle. I want to calculate the
>>>>>> diffusion coefficient for each lipid component in 3D. How to calculate
>>>>>> it
>>>>>> using g_msd (or any other tool like g_velacc)?
>>>>>>
>>>>>> Thank you for your concern
>>>>>>
>>>>>> --
>>>>>> With Best Wishes
>>>>>> Venkat Reddy Chirasani
>>>>>> --
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>>>>
>>>>
>>>>  --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>
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>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036